Holiday Notice:
The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!
The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!
Deviations from Hardy-Weinberg equilibrium

Hi,
I have a mix of heterozygous (3 samples) and inbreed samples (5 samples). I am wondering how could affect to make the SNP calling without taking into account deviations from Hardy-Weinberg equilibrium. How could I take into account these using GATK?
Best Wishes,
Eric
Best Answer
-
Sheila Broad Institute admin
@shinken
Hi Eric,The low coverage is most likely the issue. Annotation values are only used in downstream filtering tools.
Unfortunately, 4x coverage is not really that great, and you will not be able to get high confidence calls in those regions. The tools in GATK are tested on 30x coverage.
-Sheila
Answers
@shinken
Hi Eric,
What exactly is your end goal? If you use joint-genotyping, the genotypes will not be affected. The only annotations I can think of that would be affected are InbreedingCoeff and ExcessHet.
-Sheila
ok,
The problem that I am having is a very low SNP calling in inbred lines that are also low coverage lines (4x). I was wondering if the problem could be, in addition to the low coverage, the filters about deviations from the HW equilibrium.
I am calling this SNPs together with heterozygous samples (30x coverage) and I am not having problems with those ones. Do you think that the only problem is the coverage? Maybe sounds silly but using other programs such as ANGSD to obtain the genotypes I am not having this really low SNP calling in the low-coverage samples. So, I am trying to figure out what is happening.
Thank you.
@shinken
Hi Eric,
The low coverage is most likely the issue. Annotation values are only used in downstream filtering tools.
Unfortunately, 4x coverage is not really that great, and you will not be able to get high confidence calls in those regions. The tools in GATK are tested on 30x coverage.
-Sheila